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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatat-ttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
||||| |   |||||     || || |         |||     | ||| | | |||   || | | || ||  || ||||| |||        |  |||||||| |||||||| ||  |||| ||||| ||||| |||||||||||||||||||| |||| |||||||||| | |||||||| |||||||| ||||| || ||||| |
gtatatatacaggagca---acctgttagaa-----ctaaaacatatttcagtacaagtcttttcttatctagattttttctaaca--------cccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatat-ttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
||||| |   ||||   |  || || |         |||     | ||| | | |||   || | | || ||  || ||||| |||      | ||||||||||| |||||||| ||  |||| ||||| ||||| |||||||||||||||||||| |||| |||||||||| | |||||||| |||||||| ||||| || ||||| |
gtatatatacagga---ccaacctgttagaa-----ctaaaacatatttcagtacaagtcttttcttatctagattttttctaaca------cccttttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
    |   | |   |   |   |||   |    |  |   |      || |||   |  ||  |||  | | ||  ||  | || ||  |    || || || |  |||| || ||  ||||||| || |||||||  |||||||||||||||||||| | |||||| ||  |||| ||||||||||| |||||||| || ||||| |
----attgggaaatgtagaacattggcaacaagtggcagatagacagttgatt---agtttgttattttctgttgtttgattac-taattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgttt---agGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
       ||||| |    |      |  | |       |  ||||   | |||||   || |  |   | |     | ||||| |||| | || | | |||| | |   |||| || ||  |||| || || || |||||||| ||||||||||||||||||| |||||| ||  |||| |||||||||||  | ||| | || |||||||
------tagtagcaaaatactaaaaacaagtgacagaaaaacttt---tgattgctttgtcta-accttttgaccttgtctga-atacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtt-tctatgatatatttctttctgacatacctgctcttttttttgttt---agGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
         | ||      ||   ||  |||     | |||    | |  | ||   | |  | | | || |  |  | | |||| | |    ||| ||| || ||    |||| || ||  ||||||| || |||||||  || ||||||||||||||||| | |||||| ||  |||| ||||||||||| |||||||| || ||||| |
--------attgggaaatgta---gaacattggcaacaagtgccagatagactgttgattagtttgttattttctgttgtttgac-tgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 24
--gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
  || |     | ||       |||| ||| |  |   || ||  |  | ||||||   | ||||||    ||  || || | | |||   |    ||  ||||    |||| || ||| |||||||||||||||| || ||||| || ||||| ||||||| ||| || ||  |||| |||||||||||| | ||  | ||||| ||||
gggtgttttgcttggtatttgaacttaatgctgatctgctggtagtgatcttattg---aatttcta----atgcttattgc-gtcatttttttaattaattttaa--agGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCTCTGATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
--gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
  || |     | |        |||| ||| |  ||  ||| |  |  | ||||||   | ||||||    ||  || || | | |||   |  | ||  |||  |  |||| || ||| |||||||||||||||| || ||||| |||||||| ||||||| ||| || ||  ||||||||||||||||| | ||  | ||||| ||||
gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattg---aatttcta----atgcttattgc-gtcattttttttattaatttcat--agGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccct----agtctttgtttt--attgcaaagtttctatg-----atatatttc-tttctgacatacctgctcttttttttgtt--tagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
||  | |  |       |  |    |  | ||| ||||     || || | |||  ||||   |   | |||      || ||| || ||| |  | |   |  ||||||  |  ||  ||||| || ||||||||||||||||| |||||||||||||||||||| ||||||| |||| | ||  | || ||||||||||| ||||| ||||||||||| |
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgattt--ttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
||  | || ||  ||  | || ||   ||     ||   ||||  |  ||   || |||  |||| ||  | |||  |||| ||  |||     | || |  ||   ||||| || |||||||||||||| || |||||||||||||||||||||||||||| |||| | ||  | || ||||||||||| ||||| || |||||||| |
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaa--tttcaattttgtatgcctttttgtaata----tttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
  || ||  |||     ||   || || |  |     |  |  |   ||||         | || |  |  | | || | ||  ||    | | |||| |   | ||||| || ||  |||||||||||||||| || ||||||||||| |||||||| | ||| || ||  ||||||||||||||||  | ||| | ||||||||||
-aatgcagctagctattca---tttataacctcagtatgttactctatttagaatcctagtcctgt--ttgaatcctctttg--atcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
--------------------------------------------------gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
                                                  | ||    ||   |     | |||    ||      | |  | |  | || | ||    ||  ||| |  | |   || ||    ||  || | |   ||||||  |||| || ||  |||| || |||||||| || |||||||| ||||||||||||| ||| || ||  | ||||||||||||||||| ||  | || |||||||
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtat-tgatttgaattttgt--agGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
         |  ||   |||  ||  |  |||  |  | ||     | |||| |||  | |   |||| ||   | |     ||     ||   |    |||    |||| |||||| |||||||||||||| ||||||| |||||||| || || ||    || |||||  |||| ||||||||||| ||||| || || |||||||
----ttgtttttgatatcatcattactagtttggc--tggtggcattcttat-gcagtgctgg-atgagatcactttaataaaccgctttgtaatggggttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttc-tttctgacatacctgctcttttttttg-tttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
                                                | |    | |||||||  | |||| |   | | ||      ||  ||| || ||   |  |||| || ||  |||| ||||| ||||| ||||||||||| || ||| | |||  |||||| ||| |||| ||||| |||||||||||||| || || ||||
-----------------------------------------------gtaaggctatagtttctg-gttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67012270|gb|CO441019.1|CO441019
EST:     CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG                         GTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
EST: gi|32942182|gb|CF047001.1|CF047001
EST:     CTGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG                         GTTGATGACTTGGAAGAAGTCAGTGAGT
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGT
EST: gi|32942004|gb|CF046823.1|CF046823
EST:     CTGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG                         GTTGATGACTTGGAAGAAGTCAGTGAGTA
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTA
EST: gi|211133338|gb|FL220146.1|FL220146
EST:     CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG                         GTTGACGACCTGGAANAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
EST: gi|67024143|gb|CO452892.1|CO452892
EST:     CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG                         GTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
EST: gi|32942430|gb|CF047249.1|CF047249
EST:     CTGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG                         GTTGATGACTTGGAAGAAGTCAGTGAGTA
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 383

GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 482

GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
                        ttctgac  putative branch site (score: 482)
                                tacctgctcttttttt  CT-rich tract
      tttctatgatatattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA